CPAT 2.0.0 – RNA Coding Potential Assessment Tool

CPAT 2.0.0

:: DESCRIPTION

CPAT (Coding Potential Assessment Tool) is a novel alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R package

:: DOWNLOAD

 CPAT

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17.
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.
Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W.

ABMapper 2.0.4 – A suffix-array based Spliced Alignment tool

ABMapper 2.0.4

:: DESCRIPTION

ABMapper is a portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.

::DEVELOPER

ABMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Perl

:: DOWNLOAD

  ABMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):421-2. doi: 10.1093/bioinformatics/btq656. Epub 2010 Dec 17.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
Lou SK, Ni B, Lo LY, Tsui SK, Chan TF, Leung KS.

TopKCEMC 1.1 / TopKSpace 1.0 – Rank Aggregation Tool

TopKCEMC 1.1 / TopKSpace 1.0

:: DESCRIPTION

TopKCEMC is a rank aggregation tool for integrating data from multiple sources based on ranks.

TopKSpace: based on Borda’s and Markov chain methods that take spaces from the which the individual ranked lists are derived into consideration

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package

:: DOWNLOAD

 TopKCEMC , TopKSpace

:: MORE INFORMATION

Citation

Lin, S., Ding, J. (2009)
Integration of Ranked Lists via Cross Entropy Monte Carlo with Applications to mRNA and microRNA Studies.
Biometrics, 65, 9-18

Lin, S. (2010)
Space oriented rank-based data integration.
Statistical Applications in Genetics and Molecular Biolog, 20, Article 20.

FRODOCK 3.0 – Fast Rotational DOCKing tool

FRODOCK 3.0

:: DESCRIPTION

FRODOCK is able to generates very efficiently many potential predictions of how  two proteins could interact. This approximation effectively address the complexity and sampling requirements of the initial 6D docking exhaustive search by combining the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. This initial stage exhaustive docking obtain excellent accuracy results with standard benchmarks, thus you can use it directly as a first protein-protein rigid-body docking approach.

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  FRODOCK

:: MORE INFORMATION

Citation

J. I. Garzon, J. R. Lopéz-Blanco, C. Pons, J. Kovacs, R. Abagyan, J. Fernandez-Recio, P. Chacón (2009)
FRODOCK: a new approach for fast rotational protein-protein docking
Bioinformatics, 25, 2544-2551

Blast2GO 5.2.5 – Functional Annotation Tool

Blast2GO 5.2.5

:: DESCRIPTION

Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Blast2GO

:: MORE INFORMATION

Citation

A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles.
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research“,
Bioinformatics, Vol. 21, September, 2005, pp. 3674-3676.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOs
  • Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.

SmashCommunity 1.6p2 – Metagenomic Analysis and Annotation Tool

SmashCommunity 1.6p2

:: DESCRIPTION

 SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SmashCommunity

:: MORE INFORMATION

Citation

Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J. and P. Bork. (2010)
SmashCommunity: A metagenomic annotation and analysis tool,
Bioinformatics, 26, 2977-8.

 

trimAl 1.4 – Tool for Automated Alignment Trimming

trimAl 1.4

:: DESCRIPTION

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux / Windows

:: DOWNLOAD

 trimAl

:: MORE INFORMATION

Citation:

Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Bioinformatics 2009 25: 1972-1973.

AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences

AbundanceBin 1.0.1

:: DESCRIPTION

AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AbundanceBin

:: MORE INFORMATION

Citation:

Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)